Sleuthing Computers

Biomarkers play an important role in clinical cancer regimens such as prescribing the drug Lapatinib for breast cancers with HER2 gene alterations. But cancer genomes can harbor thousands of gene alterations, and most of the biomarkers currently in use consider only a single alteration. Using the data from many gene alterations could greatly improve biomarkers’ ability to guide cancer treatment, but a “brute force search” for such powerful prognostic biomarker combinations is, unfortunately, beyond the reach of even the most powerful supercomputers.

Now, however, researchers in Associate Professor of Biomedical Engineering Rachel Karchin’s lab are pioneering a computer program that has the potential to improve the accuracy of therapeutic regimens. The program “learns” to effectively comb through very large data sets, isolating combinations of gene alterations to identify new biomarkers.

A Virtual Telescope

Johns Hopkins researchers are developing a flexible, accessible, and reusable framework called a virtual telescope aimed at allowing scientists to more efficiently use huge open data sets being produced in science today.

“We’re trying to build a new scientific instrument, a virtual ‘telescope’ and ‘microscope’ of data—one that can observe data and find and extract knowledge to help you see the patterns,” says Alexander Szalay, principal investigator of the project, called Data Infrastructure Building Blocks, or DIBBS.

DIBBS should provide an important tool for scientists in areas including genomics, neuroscience, radiation oncology, and turbulence.

The team, including Whiting School computer scientists and mechanical engineers, is working under a $9.5 million, five-year National Science Foundation grant.

Improved Heart Patches

An eight-member undergraduate biomedical engineering team has snagged the top prize again at the Collegiate Inventors Competition at the U.S. Patent & Trademark Office in Alexandria, Va. Their product: a PrestoPatch that helps to treat life-threatening heart arrhythmia, an erratic heartbeat that can be fatal.

The PrestoPatch is a three-patch system to be used during defibrillation (delivering electric shocks to return a heart to its normal beat). Unlike a two-patch system currently in use, the PrestoPatch enables doctors to quickly flip a switch and change a current’s path through the body, if the first shock doesn’t help. The PrestoPatch also includes a manual tool that applies the correct amount of pressure to a patient’s chest to avoid problems with impedance of the electrical current.

TigerPaw Power

Small and wind sock shaped, the left atrial appendage perches above one of the heart’s top chambers rhythmically squeezing blood throughout body. But when the chambers don’t beat in rhythm—a condition called “atrial fibrillation”—the blood stagnates and forms clots, putting people in danger of strokes. The solution? A delicate surgery to close off the left atrial appendage.

Enter Ashik Mohan (BME ’01), director at the California-based LAAx Inc. and designer of the TigerPaw System. Cleared for use by the FDA in 2010, TigerPaw, a mechanical occlusion device, uses an extremely soft silicone fastener and two triggers to swiftly close off the faulty left atrial appendage. The device’s materials and design reduce the risk of tissue damage and bleeding often associated with other closure methods.